Bash: Identifying file based on part of filename-CodePudding

I have a folder containing paired files with names that look like this:

PB3999_Tail_XYZ_1234.bam
PB3999_PB_YWZ_5524.bam

I want to pass the files into a for loop as such:

for input in `ls PB*_Tail_.bam`; do tumor=${input%_Tail_*.bam}; $gatk Mutect2 -I $input -I$tumor${*}; done

The issue is, I can't seem to get the syntax right for the tumor input. I want it to recognise the paired file by the first part of the name PB3999_PB while ignoring the second half of the file name _YWZ_5524 that does not match.

Thank you for any help!

CodePudding user response：

Just replaced ${*} with * and added _PB_ suffix to the prefix, to the script in the question. And, renamed variables.

for tailfname in PB*_Tail_*.bam; do
    pairprefix="${tailfname%_Tail_*.bam}"
    echo command with ${tailfname} ${pairprefix}_PB_*.bam
done

Hope this helps. The name tumor sounds scary. Hope the right files are paired.

CodePudding user response：

I'm trying to fully understand what you want to do here.

If you want to extract just the first two parts, this should do:

echo "PB3999_Tail_XYZ_1234.bam" | cut -d '_' -f 1-2

That returns just the "PB3999_Tail" part.